mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 60 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | JE3692‑4 | 623,280 | 0 | A | G | 64.6% | 103.4 / 111.2 | 96 | V134A (GTA→GCA) | PP_0536 | conserved protein of unknown function |
| * | JE3692‑4 | 1,646,198 | 0 | A | C | 61.8% | 92.4 / 110.0 | 89 | T338P (ACC→CCC) | araE (Ppu opt) | |
| * | JE3692‑4 | 1,327,121 | 0 | C | T | 61.7% | 4.4 / 132.2 | 109 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | JE3692‑4 | 770,114 | 0 | T | G | 61.3% | 99.8 / 114.2 | 94 | V236G (GTG→GGG) | PP_0661 | putative Transcriptional regulator AmpR |
| * | JE3692‑4 | 4,360,849 | 0 | A | G | 56.1% | ‑1.7 / 158.5 | 107 | intergenic (‑70/+404) | PP_3820/PP_3821 | Group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | JE3692‑4 | 783,036 | 0 | A | G | 55.7% | 41.6 / 140.3 | 97 | F964L (TTC→CTC) | PP_0672 | Sensory box protein |
| * | JE3692‑4 | 1,849,619 | 0 | G | C | 54.7% | 34.5 / 163.5 | 95 | N269K (AAC→AAG) | PP_1650 | Sensor protein GacS |
| * | JE3692‑4 | 6,107,039 | 0 | T | C | 43.2% | 32.8 / 113.0 | 81 | intergenic (‑38/‑152) | PP_5347/PP_5348 | pyruvate carboxylase subunit A/Transcriptional regulator, LysR family |
| * | JE3692‑4 | 1,646,010 | 0 | A | G | 43.0% | 52.4 / 114.4 | 86 | N275S (AAC→AGC) | araE (Ppu opt) | |
| * | JE3692‑4 | 699,722 | 0 | A | G | 42.6% | 53.6 / 90.7 | 68 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | JE3692‑4 | 3,636,954 | 0 | G | C | 40.4% | 29.7 / 36.7 | 51 | G226G (GGC→GGG) | PP_3195 | conserved protein of unknown function |
| * | JE3692‑4 | 195,634 | 0 | C | T | 38.7% | 234.6 / 214.0 | 168 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 196,351 | 0 | C | G | 37.4% | 230.9 / 252.8 | 188 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 3,446,934 | 0 | G | A | 37.2% | 69.1 / 90.8 | 78 | G9S (GGC→AGC) | PP_3053 | Pyocin R2_PP, baseplate protein |
| * | JE3692‑4 | 2,184,203 | 0 | T | C | 37.0% | 117.6 / 63.8 | 92 | N269N (AAT→AAC) | PP_1931 | conserved protein of unknown function |
| * | JE3692‑4 | 4,820,324 | 0 | A | C | 35.3% | 19.9 / 16.7 | 18 | intergenic (‑289/‑266) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | JE3692‑4 | 187,508 | 0 | T | C | 34.0% | 117.5 / 100.0 | 97 | L107P (CTG→CCG) | PP_0164 | conserved protein of unknown function |
| * | JE3692‑4 | 324,670 | 0 | C | T | 33.3% | 102.8 / 43.7 | 73 | intergenic (‑430/‑45) | PP_0267/PP_0268 | putative Outer membrane ferric siderophore receptor/outer‑membrane porin D |
| * | JE3692‑4 | 4,820,325 | 0 | A | G | 33.3% | 18.5 / 14.3 | 18 | intergenic (‑290/‑265) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | JE3692‑4 | 196,390 | 0 | T | C | 33.1% | 206.3 / 136.7 | 136 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 776 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | JE3692‑4 | = 3218138 | 0 (0.000) | 38 (0.400) | 31/196 | 3.4 | 100% | coding (337/567 nt) | PP_2816 | putative Transcriptional regulator NfxB |
| ? | JE3692‑4 | 3286212 = | 0 (0.000) | coding (526/1455 nt) | xylB (Ppu opt) | ||||||
| * | ? | JE3692‑4 | = 652782 | 84 (0.880) | 31 (0.410) | 23/156 | 3.5 | 47.7% | coding (1961/1962 nt) | PP_0562 | Methyl‑accepting chemotaxis protein CtpL |
| ? | JE3692‑4 | = 4820303 | 1 (0.010) | intergenic (‑268/‑287) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | JE3692‑4 | = 1848703 | 59 (0.620) | 31 (0.340) | 26/188 | 4.1 | 35.9% | coding (1723/2754 nt) | PP_1650 | Sensor protein GacS |
| ? | JE3692‑4 | 1848708 = | 54 (0.590) | coding (1718/2754 nt) | PP_1650 | Sensor protein GacS | |||||
| * | ? | JE3692‑4 | = 4820323 | 12 (0.130) | 26 (0.340) | 20/156 | 4.2 | 50.7% | intergenic (‑288/‑267) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | JE3692‑4 | = 6000025 | 41 (0.540) | intergenic (+243/‑303) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | JE3692‑4 | = 4820323 | 12 (0.130) | 27 (0.320) | 20/172 | 4.9 | 42.0% | intergenic (‑288/‑267) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | JE3692‑4 | 5999841 = | 64 (0.760) | intergenic (+59/‑487) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | JE3692‑4 | = 652783 | 85 (0.890) | 24 (0.390) | 12/126 | 5.3 | 46.3% | coding (1960/1962 nt) | PP_0562 | Methyl‑accepting chemotaxis protein CtpL |
| ? | JE3692‑4 | 4820353 = | 1 (0.020) | intergenic (‑318/‑237) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | JE3692‑4 | 4820318 = | 17 (0.180) | 25 (0.360) | 13/144 | 5.8 | 46.9% | intergenic (‑283/‑272) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | JE3692‑4 | 5999855 = | 44 (0.630) | intergenic (+73/‑473) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | JE3692‑4 | 173166 = | NA (NA) | 18 (0.190) | 17/194 | 6.8 | NA | intergenic (+256/‑37) | PP_16SA/PP_23SA | 16S ribosomal RNA/23S ribosomal RNA |
| ? | JE3692‑4 | 173218 = | NA (NA) | noncoding (16/2902 nt) | PP_23SA | 23S ribosomal RNA | |||||
| * | ? | JE3692‑4 | = 4820320 | 20 (0.210) | 19 (0.220) | 14/180 | 7.2 | 34.1% | intergenic (‑285/‑270) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | JE3692‑4 | 4820424 = | 55 (0.630) | intergenic (‑389/‑166) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | JE3692‑4 | 336300 = | 57 (0.600) | 5 (0.090) +43 bp |
5/110 | 7.7 | 9.8% | intergenic (+148/+245) | PP_0278/PP_0279 | conserved protein of unknown function/conserved protein of unknown function |
| ? | JE3692‑4 | = 661000 | 107 (1.120) | intergenic (+132/‑35) | PP_0567/PP_0568 | Biosynthetic arginine decarboxylase/conserved protein of unknown function | |||||